I just saw these e-mails. Did you try to run 'make install' as the same user you ran 'make all'? At least on Mac OS X you have to create the directory (e.g. /usr/local/tpp/) first manually, change permissions e.g. to 777, run 'make install' as the same user who ran 'make all' and then change the permissions back to whatever is more appropriate. I guess 'make install' needs environment variables set during 'make all'.
Maybe, that helps. Ulrich On Sep 25, 2009, at 7:30 PM, Natalie Tasman wrote: > That's another good suggestion. I didn't see Brian's message when I > replied today :) > > > On Sep 25, 2009, at 8:00 AM, Brian Pratt wrote: > >> I'd say next step is try to perform a build on a different computer >> and transfer the binaries to the computer you want to use. There's >> something very peculiar about that system, but hopefully it won't >> affect TPPs ability to run once it has been built elsewhere. >> >> On Thu, Sep 24, 2009 at 10:41 PM, Eliza <blond...@googlemail.com> >> wrote: >> >> Any more suggestions? There is quite a lot of interest in getting >> TPP >> running in the lab and at this point I am not sure how to proceed. >> >> On Sep 18, 8:15 pm, Brian Pratt <brian.pr...@insilicos.com> wrote: >> > (FWIW, Ubuntu is a flavor of Debian) >> > >> > That's interesting - does "make clean all" work after your first >> "make >> > all"? It sounds like the build is somehow changing the >> environment, or >> > maybe even its own makefiles... >> > >> > On Thu, Sep 17, 2009 at 11:45 PM, Eliza <blond...@googlemail.com> >> wrote: >> > >> > > I haven't tried your suggestion of running it on another distro >> yet >> > > Natalie, but I did get the latest version when that was >> announced and >> > > I got a little bit further. I was able to run 'make all' >> without any >> > > errors, but when I run try to run 'make install' I'm back with >> the >> > > error message "Makefile.incl:431: /Makefile.pwiz.incl: No such >> file or >> > > directory >> > > make: *** No rule to make target `/Makefile.pwiz.incl'. Stop." >> > >> > > I am not using Ubuntu, but Debian. >> > >> > > On Sep 4, 8:40 pm, Natalie Tasman <natalie.tas...@insilicos.com> >> > > wrote: >> > > > Hi Eliza, >> > >> > > > At this point, it might be worthwhile trying to compile the >> TPP on >> > > > another linux distribution that works well. For example, >> Ubuntu >> > > > 8.04. Then, I'd be sure to run the correct "install >> prerequisites" >> > > > file from tpp/installer_linux to make sure all the required >> system >> > > > packages are installed. >> > >> > > > Then again, it wouldn't hurt to run the correct "install >> > > > prerequisites" for your own system. Currently, the Ubuntu >> 9.04 script >> > > > seems to work for 9.10 also, if you're using that. >> > >> > > > Good luck, >> > >> > > > Natalie >> > >> > > > On Sep 4, 2009, at 1:05 AM, Eliza wrote: >> > >> > > > > Mike - having an empty Makefile.config.incl didn't fix >> anything. I am >> > > > > still getting the error: make: *** No rule to make target `/ >> > > > > Makefile.pwiz.incl'. Stop. >> > >> > > > > On Sep 1, 10:21 pm, Mike Coleman <tutu...@gmail.com> wrote: >> > > > >> Okay, this turned out to be useful. It appears that the >> contents of >> > > > >> your file 'Makefile.config.incl' is including itself (it >> appears to >> > > > >> be >> > > > >> a copy of 'Makefile.incl'). This recurses about 1000 >> times, at which >> > > > >> point you hit the file handle limit. The resulting error is >> > > > >> apparently ignored due to the '-include'. >> > >> > > > >> So, either make 'Makefile.config.incl' an empty file, or >> otherwise I >> > > > >> think it should be just a short file including a few >> variable >> > > > >> definitions. Also, verify that neither of these files is >> a symbolic >> > > > >> or hard link to the other. >> > >> > > > >> Probably this will fix things, or at least move things >> forward. >> > >> > > > >> Mike >> > >> > > > >> On Aug 31, 2:34 am, Eliza <blond...@googlemail.com> wrote: >> > >> > > > >>> OK I have added make.strace.gz to the file uploads. >> > >> > > > >>> On Aug 28, 6:34 pm, Mike Coleman <tutu...@gmail.com> wrote: >> > >> > > > >>>> Okay, if you really want to bring out the big guns, do >> something >> > > > >>>> like >> > > > >>>> this >> > >> > > > >>>> $ strace -f -s 1024 -v -o make.strace make >> > >> > > > >>>> and put the resulting 'make.strace' log somewhere where >> we can >> > > > >>>> look at >> > > > >>>> it. I think this is erroring out pretty quickly, so >> hopefully that >> > > > >>>> log won't be too huge. No promises, but this may very >> well clarify >> > > > >>>> what's going wrong. >> > >> > > > >>>> You'll have to install the strace package if it's not >> already >> > > > >>>> present. >> > >> > > > >>>> Mike >> > >> > > > >>>> On Aug 28, 4:59 am, Eliza <blond...@googlemail.com> wrote: >> > >> > > > >>>>> That doesn't make any difference. >> > >> > > > >>>>> On Aug 27, 8:12 pm, "Brian Pratt" >> <brian.pr...@insilicos.com> >> > > > >>>>> wrote: >> > >> > > > >>>>>> Yeah, that's what we use here too. Perhaps you could >> try it as >> > > > >>>>>> a different, >> > > > >>>>>> newly created user? It sounds like there is something >> peculiar >> > > > >>>>>> about your >> > > > >>>>>> shell setup. >> > >> > > > >>>>>> -----Original Message----- >> > > > >>>>>> From: spctools-discuss@googlegroups.com >> > >> > > > >>>>>> [mailto:spctools-disc...@googlegroups.com] On Behalf >> Of Eliza >> > > > >>>>>> Sent: Thursday, August 27, 2009 12:13 AM >> > > > >>>>>> To: spctools-discuss >> > > > >>>>>> Subject: [spctools-discuss] Re: Failure with make >> > >> > > > >>>>>> Bash >> > >> > > > >>>>>> On Aug 20, 11:55 pm, "Brian Pratt" >> <brian.pr...@insilicos.com> >> > > > >>>>>> wrote: >> > > > >>>>>>> We basically tried that already: Eliza says the >> suggested >> > >> > > > >>>>>>> export PWD=/opt/trans_proteomic_pipeline/src ; make >> all install >> > >> > > > >>>>>>> did not work. She also tried the "SRC_ROOT= $(shell >> pwd)" >> > > > >>>>>>> change to the >> > > > >>>>>>> makefile. There's something deeper going on. >> > >> > > > >>>>>>> Eliza, what shell do you use? I do see from googling >> that >> > > > >>>>>>> $PWD might be >> > > > >>>>>>> bash-specific, possibly there are other unintended bash >> > > > >>>>>>> dependencies. >> > >> > > > >>>>>>> Brian >> > >> > > > >>>>>>> -----Original Message----- >> > > > >>>>>>> From: spctools-discuss@googlegroups.com >> > >> > > > >>>>>>> [mailto:spctools-disc...@googlegroups.com] On Behalf >> Of Mike >> > > > >>>>>>> Coleman >> > > > >>>>>>> Sent: Thursday, August 20, 2009 1:26 PM >> > > > >>>>>>> To: spctools-discuss >> > > > >>>>>>> Subject: [spctools-discuss] Re: Failure with make >> > >> > > > >>>>>>> Eliza, >> > >> > > > >>>>>>> I'mstill suspicious about the $PWD thing. If you're >> running >> > > > >>>>>>> 'make' >> > > > >>>>>>> normally, you might try something like >> > >> > > > >>>>>>> $ PWD=$(pwd) make ... >> > >> > > > >>>>>>> instead of just >> > >> > > > >>>>>>> $ make ... >> > >> > > > >>>>>>> to see whether that improves your situation. >> Alternatively, >> > > > >>>>>>> for the >> > > > >>>>>>> 'root' steps, you could do something like >> > >> > > > >>>>>>> $ sudo PWD=$(pwd) make ... >> > >> > > > >>>>>>> Mike >> >> >> >> > > > > --~--~---------~--~----~------------~-------~--~----~ You received this message because you are subscribed to the Google Groups "spctools-discuss" group. To post to this group, send email to spctools-discuss@googlegroups.com To unsubscribe from this group, send email to spctools-discuss+unsubscr...@googlegroups.com For more options, visit this group at http://groups.google.com/group/spctools-discuss?hl=en -~----------~----~----~----~------~----~------~--~---
